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Rationale The recent progress in micro‐scale isotopic analytical techniques for otoliths has enabled the reconstruction of the experienced water temperature history of fish in every few days resolution using the stable oxygen isotope ratio (δ18O) of otoliths. We aimed to improve those techniques and extract the daily δ18O records of otoliths formed during the juvenile period. Methods Growth rings were formed daily in fish otoliths. We precisely distinguished the daily rings in otoliths of Japanese jack mackerel Trachurus japonicus, and milled them along daily growth rings using a high‐spatial resolution micromilling system (Geomill326). Then, we determined the stable carbon and oxygen (δ13C, δ18O) isotopic compositions using a high‐precision micro‐scale isotopic analytical system (MICAL3c with IsoPrime 100). Results We successfully milled each daily ring with width ranging from 14.0 to 62.9 μm (average 27.0 μm) during the high growth period (30–70 days after hatching), and determined the isotopic compositions of otolith aragonite. Conclusions Our improved micro‐scale analytical method is the first to determine the daily δ18O history of fish otoliths. By using our method together with the δ18O – water temperature equation, the daily history of experienced water temperature can be elucidated. Our high‐resolution milling and analytical technique can also be applied to high‐resolution isotope analysis for stalactites, clams, and corals.